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This Week in PNAS: Oct 6, 2015

In the early, online edition of the Proceedings of the National Academy of Science, an international team led by investigators in the UK, Malaysia, and Saudi Arabia look at population structure in the Plasmodium knowlesi parasite, through genome sequencing on four dozen clinical isolates from Malaysian Borneo and five lab-based lines that originated from the Malaysian Peninsula and the Philippines several decades ago. From these sequences, the researchers identified more than 975,000 high-quality SNPs in P. knowlesi, including almost 9,300 fixed SNP differences that distinguished a cluster of 38 clinical isolates from the remaining 10 clinical isolates. GenomeWeb has more on the study, here.

Researchers from the University of Wisconsin-Madison, the John Innes Centre in Norwich, and elsewhere describe apparent pre-adaptations in the algal ancestors of land plants. Using hundreds of plant and algal transcriptome sequences, together with genome sequences for 10 green algae or basal land plant species, the team performed a phylogenetic analysis that pointed to the presence of a regulator of plant-fungal interactions prior to the appearance of early land plants. From these and other findings, the study's authors argue that "the most recent common ancestor of extant land plants and green algae was pre-adapted for symbiotic associations."

Finally, a team from Finland, Germany, the Netherlands, and the UK track transcription dynamics with the help of a model that takes into account transcriptional activation and messenger RNA accumulation patterns. When they used this approach to analyze RNA polymerase II chromatin immunoprecipitation sequencing data and messenger RNA-seq data collected over time in the MCF-7 breast cancer cell line, the researchers detected genes with delays between the end of transcription and the start of mRNA production — a pattern that was more common in short genes, for example. "The distribution of intronic reads suggests that these delays are required for splicing to be completed," the team writes. "Understanding such delays is essential for understanding how a rapid cellular response is regulated."